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David Gresham - Publications

Affiliations: 
Biology New York University, New York, NY, United States 
Area:
Evolution and Development Biology, Genetics
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Avecilla G, Spealman P, Matthews J, Caudal E, Schacherer J, Gresham D. Copy number variation alters local and global mutational tolerance. Genome Research. PMID 37652668 DOI: 10.1101/gr.277625.122  0.323
2020 Sun S, Baryshnikova A, Brandt N, Gresham D. Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states. Molecular Systems Biology. 16: e9167. PMID 32449603 DOI: 10.15252/Msb.20199167  0.364
2020 Spealman P, Burrell J, Gresham D. Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy. Nucleic Acids Research. PMID 32255181 DOI: 10.1093/Nar/Gkaa206  0.309
2020 Jackson C, Gresham D. A Bright IDEA. Molecular Systems Biology. 16: e9502. PMID 32253808 DOI: 10.15252/Msb.20209502  0.326
2020 Jackson CA, Castro DM, Saldi GA, Bonneau R, Gresham D. Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. Elife. 9. PMID 31985403 DOI: 10.7554/Elife.51254  0.415
2019 Lauer S, Gresham D. An evolving view of copy number variants. Current Genetics. PMID 31076843 DOI: 10.1007/S00294-019-00980-0  0.416
2019 Athanasiadou R, Neymotin B, Brandt N, Wang W, Christiaen L, Gresham D, Tranchina D. A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory. Plos Computational Biology. 15: e1006794. PMID 30856174 DOI: 10.1371/Journal.Pcbi.1006794  0.318
2019 Jackson CA, Castro DM, Saldi G, Bonneau R, Gresham D. Author response: Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments Elife. DOI: 10.7554/Elife.51254.Sa2  0.353
2019 Gresham D, Rancati G. Meeting report: Experimental and evolutionary approaches to yeast and other organisms 2018 G3: Genes, Genomes, Genetics. 9: 635-638. DOI: 10.1534/G3.118.201003  0.309
2018 Lauer S, Avecilla G, Spealman P, Sethia G, Brandt N, Levy SF, Gresham D. Single-cell copy number variant detection reveals the dynamics and diversity of adaptation. Plos Biology. 16: e3000069. PMID 30562346 DOI: 10.1371/Journal.Pbio.3000069  0.424
2018 Hong J, Brandt N, Abdual-Rahman F, Yang AWH, Hughes TR, Gresham D. An incoherent feedforward loop facilitates adaptive tuning of gene expression. Elife. 7. PMID 29620523 DOI: 10.7554/Elife.32323  0.577
2018 Hong J, Brandt N, Abdul-Rahman F, Yang A, Hughes T, Gresham D. Author response: An incoherent feedforward loop facilitates adaptive tuning of gene expression Elife. DOI: 10.7554/Elife.32323.017  0.551
2017 Hong J, Gresham D. Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing. Biotechniques. 63: 221-226. PMID 29185922 DOI: 10.2144/000114608  0.585
2017 Ziv N, Shuster BM, Siegal ML, Gresham D. Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth. Genetics. PMID 28495957 DOI: 10.1534/Genetics.116.195180  0.387
2016 Neymotin B, Ettore V, Gresham D. Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae. G3 (Bethesda, Md.). PMID 27633789 DOI: 10.1534/G3.116.032276  0.312
2016 Airoldi EM, Miller D, Athanasiadou R, Brandt N, Abdul-Rhaman F, Neymotin B, Hashimoto T, Bahmani T, Gresham D. Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen. Molecular Biology of the Cell. PMID 26941329 DOI: 10.1091/Mbc.E14-05-1013  0.366
2015 Gresham D. Evolution: Fitness tracking for adapting populations. Nature. 519: 164-5. PMID 25731163 DOI: 10.1038/Nature14207  0.31
2015 Gresham D, Hong J. The functional basis of adaptive evolution in chemostats. Fems Microbiology Reviews. 39: 2-16. PMID 25098268 DOI: 10.1111/1574-6976.12082  0.595
2014 Gresham D, Dunham MJ. The enduring utility of continuous culturing in experimental evolution. Genomics. 104: 399-405. PMID 25281774 DOI: 10.1016/J.Ygeno.2014.09.015  0.315
2014 Hong J, Gresham D. Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments. Plos Genetics. 10: e1004041. PMID 24415948 DOI: 10.1371/Journal.Pgen.1004041  0.619
2014 Robinson DG, Chen W, Storey JD, Gresham D. Design and analysis of Bar-seq experiments. G3 (Bethesda, Md.). 4: 11-8. PMID 24192834 DOI: 10.1534/G3.113.008565  0.348
2013 Ziv N, Brandt NJ, Gresham D. The use of chemostats in microbial systems biology. Journal of Visualized Experiments : Jove. PMID 24145466 DOI: 10.3791/50168  0.363
2013 Ziv N, Siegal ML, Gresham D. Genetic and nongenetic determinants of cell growth variation assessed by high-throughput microscopy. Molecular Biology and Evolution. 30: 2568-78. PMID 23938868 DOI: 10.1093/Molbev/Mst138  0.341
2013 Geiler-Samerotte KA, Bauer CR, Li S, Ziv N, Gresham D, Siegal ML. The details in the distributions: why and how to study phenotypic variability. Current Opinion in Biotechnology. 24: 752-9. PMID 23566377 DOI: 10.1016/J.Copbio.2013.03.010  0.351
2012 Torbensen R, Møller HD, Gresham D, Alizadeh S, Ochmann D, Boles E, Regenberg B. Amino acid transporter genes are essential for FLO11-dependent and FLO11-independent biofilm formation and invasive growth in Saccharomyces cerevisiae. Plos One. 7: e41272. PMID 22844449 DOI: 10.1371/Journal.Pone.0041272  0.334
2011 Abbey D, Hickman M, Gresham D, Berman J. High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains. G3 (Bethesda, Md.). 1: 523-30. PMID 22384363 DOI: 10.1534/G3.111.000885  0.314
2011 Gresham D, Boer VM, Caudy A, Ziv N, Brandt NJ, Storey JD, Botstein D. System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics. 187: 299-317. PMID 20944018 DOI: 10.1534/Genetics.110.120766  0.389
2010 Gresham D, Usaite R, Germann SM, Lisby M, Botstein D, Regenberg B. Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus. Proceedings of the National Academy of Sciences of the United States of America. 107: 18551-6. PMID 20937885 DOI: 10.1073/Pnas.1014023107  0.378
2010 Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, Kruglyak L. Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature. 464: 1039-42. PMID 20393561 DOI: 10.1038/Nature08923  0.348
2010 Gresham D, Curry B, Ward A, Gordon DB, Brizuela L, Kruglyak L, Botstein D. Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proceedings of the National Academy of Sciences of the United States of America. 107: 1482-7. PMID 20080586 DOI: 10.1073/Pnas.0913883107  0.335
2009 Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, et al. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nature Biotechnology. 27: 369-77. PMID 19349972 DOI: 10.1038/Nbt.1534  0.357
2009 Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. Plos Computational Biology. 5: e1000257. PMID 19119411 DOI: 10.1371/Journal.Pcbi.1000257  0.385
2008 Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, Dunham MJ. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. Plos Genetics. 4: e1000303. PMID 19079573 DOI: 10.1371/Journal.Pgen.1000303  0.415
2008 Gresham D, Kruglyak L. Rise of the machines. Plos Genetics. 4: e1000134. PMID 18670625 DOI: 10.1371/Journal.Pgen.1000134  0.312
2008 Gresham D, Dunham MJ, Botstein D. Comparing whole genomes using DNA microarrays. Nature Reviews. Genetics. 9: 291-302. PMID 18347592 DOI: 10.1038/Nrg2335  0.348
2008 Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Molecular Biology of the Cell. 19: 352-67. PMID 17959824 DOI: 10.1091/Mbc.E07-08-0779  0.353
2007 Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L. Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. Plos One. 2: e322. PMID 17389913 DOI: 10.1371/Journal.Pone.0000322  0.326
2006 Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, Dunham MJ. Global mapping of transposon location. Plos Genetics. 2: e212. PMID 17173485 DOI: 10.1371/Journal.Pgen.0020212  0.367
2006 Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, Kruglyak L. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science (New York, N.Y.). 311: 1932-6. PMID 16527929 DOI: 10.1126/Science.1123726  0.368
2004 Morar B, Gresham D, Angelicheva D, Tournev I, Gooding R, Guergueltcheva V, Schmidt C, Abicht A, Lochmüller H, Tordai A, Kalmár L, Nagy M, Karcagi V, Jeanpierre M, Herczegfalvi A, et al. Mutation history of the Roma/Gypsies American Journal of Human Genetics. 75: 596-609. PMID 15322984 DOI: 10.1086/424759  0.344
2001 Gresham D, Morar B, Underhill PA, Passarino G, Lin AA, Wise C, Angelicheva D, Calafell F, Oefner PJ, Shen P, Tournev I, de Pablo R, Kuĉinskas V, Perez-Lezaun A, Marushiakova E, et al. Origins and divergence of the Roma (gypsies). American Journal of Human Genetics. 69: 1314-31. PMID 11704928 DOI: 10.1086/324681  0.339
2000 Kalaydjieva L, Gresham D, Gooding R, Heather L, Baas F, de Jonge R, Blechschmidt K, Angelicheva D, Chandler D, Worsley P, Rosenthal A, King RH, Thomas PK. N-myc downstream-regulated gene 1 is mutated in hereditary motor and sensory neuropathy-Lom. American Journal of Human Genetics. 67: 47-58. PMID 10831399 DOI: 10.1046/J.1529-8027.2001.01008-16.X  0.34
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